Scottish ministers have revealed the UK Covid Inquiry first asked them for relevant WhatsApp messages nine months ago.
The first minister said last week his government was only asked to submit WhatsApp group messages related to the pandemic in September.
Opposition parties have accused Humza Yousaf and his deputy, Shona Robison, of misleading parliament.
The Scottish government said it was co-operating fully with the inquiry.
Deputy First Minister Shona Robison published a detailed timeline of events in a written statement to the Scottish Parliament following a request from the UK Covid Inquiry.
the Scottish government was initially asked on 4 November 2022 about WhatsApps and other "informal messaging systems" via a draft request under Rule 9 of the Inquiry Rules 2006.
On 2 February 2023 the inquiry sent a final version of the Rule 9 request. This included requests for WhatsApp messages relating to the pandemic response and decision-making.
Ms Robison said similar requests were received in February and March, seeking evidence, including WhatsApp messages, from Scottish government directorates.
She said draft responses were sent "throughout Spring 2023", in which the government insisted all "key decisions and decision-making were recorded on the Scottish government corporate record". No WhatsApp messages were included as part of those responses.
Those draft responses were finalised in June but the inquiry asked for further information about the use of WhatsApp groups "concerned with the Covid-19 response".
Ms Robison said that once information concerning those groups was provided, the inquiry then asked in September for those messages to be handed over.
The Scottish government said that privacy concerns meant it required a formal request under Section 21 of the Inquiries Act 2005 before it was able to submit more than 14,000 messages by a 6 November deadline.
This "corporate" submission did not include minister-to-minister conversations and was restricted to conversations of three or more people involving at least one civil servant.
The Scottish government said Mr Yousaf made his final submission to the UK inquiry on Monday. It is understood to run to around 100 pages.
He has also handed over his Covid WhatsApp messages which he is said to have retrieved from an old phone handset.
Mr Yousaf said previously that when the inquiry asked in June for details of the WhatsApp groups, it did not request the messages themselves.
In response to a question from Anas Sarwar last week, he said: "It is crucial to say that, when the UK government inquiry asked us in June for details of the various WhatsApp groups concerning Covid 19, it did not request the messages themselves.
"The messages were asked for in September, just a matter of weeks ago.
"The Scottish government then asked for a Section 21 order because of the personal information in some of those messages, and that was received. Now, of course, we will meet the deadline of 6 November to hand over 14,000 messages in unredacted form."
Scottish Tory leader Douglas Ross said: "It's clear that the first minister and deputy first minister misled parliament last week when they claimed that ministers were only asked to hand over WhatsApp messages in the last few weeks."
Scottish Labour deputy leader Jackie Baillie said the newly-published timeline contradicted their statements.
"The only thing clearer is the extent to which this shambolic government has lost control trying to cover up the truth and obstruct those seeking it," she said. "It begs the question, what do they have to hide. "Meanwhile the public are no clearer on who has complied with the do not destroy order and how many senior ministers and officials deleted messages."
There are two interesting elements to this timeline.
The first is the fact the inquiry has asked the Scottish government to put it on the public record in the first place.
Although messages have now been handed over, this shows there was quite a bit of a back-and-forth - and perhaps underlines why the inquiry's lead counsel felt the need to raise the matter in a public hearing.
The second is the difficulty it could pose for Humza Yousaf, given his past statements about when requests were made.
You can see the path the government is attempting to weave through, by taking a narrow reading of each request - contending that the first one was about specific messages relating to decision-making, and that the next one was just asking about the existence of groups.
The question is how well this sits with the actual request from February, which asked for "any communications relating to key decisions".
Opposition MSPs are reading that as a much broader request than was previously suggested by ministers.
In a row with many moving parts, that is likely to be the element which grips Holyrood in the coming days.
The UK inquiry has asked to see the WhatsApp messages of 70 officials, medical chiefs, ministers and former ministers, and identified 137 messaging groups that could contain relevant information.
However, the inquiry's counsel, Jamie Dawson KC, said "very few" of the messages it was interested in appeared to have been retained.
The Scottish inquiry issued a "do not destroy" order at the beginning of August 2022, meaning it could be an offence for witnesses to have deleted Covid-related messages after that date.
In June this year, Mr Yousaf told MSPs that all requested material would "absolutely" be handed over to the Covid inquiries in full.
Senior members of the Scottish government's leadership team from the pandemic - including Ms Sturgeon and ex-deputy first minister John Swinney - have been accused of deleting messages.
Both have said they would comply with the inquiries but refused to deny removing messages.
National clinical director Jason Leitch has also been accused of deleting messages during the pandemic, while chief medical officer Prof Sir Gregor Smith is alleged to have used an auto-delete function on WhatsApp messages.
Both were approached for comment.